Cells and organisms function through highly complex networks of genes, proteins, and metabolites, working in concert. Understanding the function and regulation of these systems is a major goal of biomedical and bioengineering research in the post-genomic era. These multivariable systems are highly dynamic, and their responses are nonlinear. Therefore, traditional methods of studying one protein or pathway in isolation often fail. A new paradigm is required to understand the mechanisms by which interrelated pathways and networks of biochemical activities regulate cell functions and control cellular responses. Methods for pathway analysis and reconstruction are well established. What is needed now is to combine biological/biotechnology and systems engineering approaches, creating research instruments to integrate these methods and take value from them. We propose a synergistic combination of modeling and experimentation to develop and test quantitative tools for characterizing and controlling the response of yeast cells to stress. This project proposal describes the development and application of mathematical tools for modeling the intracellular phenomena of biological processes, and the development of molecular-level sensors for real-time acquisition of data during cell growth and protein expression. The utility of these research instruments will be evaluated on the unfolded protein response in the yeast Saccharomyces cerevisiae, during expression of a single-chain antibody.